From 0727619e069f40f5e4094b16a206616c0f0220d0 Mon Sep 17 00:00:00 2001 From: Peter Van Dyken Date: Wed, 2 Oct 2024 16:34:20 -0400 Subject: [PATCH] Update dependencies Major updates for sphinx --- .readthedocs.yml | 2 +- poetry.lock | 2264 ++++++++++++----------- pyproject.toml | 34 +- snakebids/plugins/cli_config.py | 4 +- snakebids/tests/test_generate_inputs.py | 16 +- typings/pyfakefs/fake_filesystem.pyi | 3 +- 6 files changed, 1223 insertions(+), 1100 deletions(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 1a248af5..1c4a0616 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -20,7 +20,7 @@ formats: build: os: 'ubuntu-22.04' tools: - python: '3.11' + python: '3.12' jobs: post_checkout: - (git fetch --tags) || exit 183 diff --git a/poetry.lock b/poetry.lock index 5af5bc9d..b763e8ff 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,13 +2,13 @@ [[package]] name = "alabaster" -version = "0.7.13" -description = "A configurable sidebar-enabled Sphinx theme" +version = 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--- a/pyproject.toml +++ b/pyproject.toml @@ -34,7 +34,7 @@ patterns = [ python = ">=3.8,<4.0" # core dep with high breakage potential given plans for redesign, so # keep upper limit -pybids = ">=0.16.0,<0.17" +pybids = ">=0.16.0,<0.18" snakemake = [ { version = ">=5.28.0,<8", python = "<3.11" }, { version = ">=7.18.2", python = ">=3.11" }, @@ -81,7 +81,7 @@ pluggy = ">=1.3" [tool.poetry.group.dev.dependencies] pytest = "^8" pytest-mock = "^3.7.0" -poethepoet = "^0.27" +poethepoet = "^0.29" pre-commit = "^3.0.0" # a mkinit dep has the 'platform_system == "Windows"' as a marker on an incompatible dependency # (pydantic<2.0 cf copier), so set the inverse as a marker here so mkinit can @@ -92,8 +92,9 @@ pytest-benchmark = "^4.0.0" pyfakefs = "^5.1.0" pyparsing = "^3.0.9" pathvalidate = "^3.0.0" -pyright = "^1.1.370" -ruff = "^0.5" +# Avoid bug in 1.1.388 (see https://github.com/microsoft/pyright/issues/9136) +pyright = "1.1.377" +ruff = "^0.6" pytest-xdist = "^3.3.1" pytest-split = [ { version = "^0.8.1", python = "3.8" }, @@ -106,21 +107,16 @@ docstring-parser = "^0.16" [tool.poetry.group.docs.dependencies] -sphinx = "^7" -sphinx-argparse = "^0.4.0" -sphinxcontrib-asciinema = "^0.4" -myst-parser = "^3" -furo = "^2024.4.27" -sphinx-copybutton = "^0.5.2" -sphinx-reredirects = "^0.1.3" -sphinx-design = [ - { version = "^0.5.0", python = "3.8" }, - { version = "^0.6", python = ">=3.9" }, -] -sphinx-autobuild = [ - { version = "^2021.03.14", python = "3.8" }, - { version = "^2024.02.04", python = ">=3.9" }, -] +sphinx = { version = "^8", python = ">=3.10" } +sphinx-argparse = { version = "^0.4.0", python = ">=3.10" } +sphinxcontrib-asciinema = { version = "^0.4", python = ">=3.10" } +myst-parser = { version = "^4", python = ">=3.10" } +furo = { version = "^2024.4.27", python = ">=3.10" } +sphinx-copybutton = { version = "^0.5.2", python = ">=3.10" } +sphinx-reredirects = { version = "^0.1.3", python = ">=3.10" } +sphinx-design = { version = "^0.6", python = ">=3.10" } +sphinx-autobuild = { version = "^2024.02.04", python = ">=3.10" } + [tool.poetry.scripts] snakebids = "snakebids.admin:main" diff --git a/snakebids/plugins/cli_config.py b/snakebids/plugins/cli_config.py index 582a889a..9b82077a 100644 --- a/snakebids/plugins/cli_config.py +++ b/snakebids/plugins/cli_config.py @@ -3,7 +3,7 @@ import argparse import re from pathlib import Path -from typing import Any +from typing import Any, Callable import attrs @@ -38,7 +38,7 @@ def _make_underscore_dash_aliases(name: str) -> set[str]: return {name} -def _find_type(name: str, *, yamlsafe: bool = True) -> type[Any]: +def _find_type(name: str, *, yamlsafe: bool = True) -> Callable[[Any], Any]: import importlib if name == "Path": diff --git a/snakebids/tests/test_generate_inputs.py b/snakebids/tests/test_generate_inputs.py index 2f989a71..5278f361 100644 --- a/snakebids/tests/test_generate_inputs.py +++ b/snakebids/tests/test_generate_inputs.py @@ -13,7 +13,16 @@ import warnings from collections import defaultdict from pathlib import Path, PosixPath -from typing import Any, Iterable, Literal, NamedTuple, TypedDict, TypeVar, cast +from typing import ( + TYPE_CHECKING, + Any, + Iterable, + Literal, + NamedTuple, + TypedDict, + TypeVar, + cast, +) import attrs import more_itertools as itx @@ -56,6 +65,9 @@ from snakebids.utils.containers import MultiSelectDict from snakebids.utils.utils import DEPRECATION_FLAG, BidsEntity, BidsParseError +if TYPE_CHECKING: + from _typeshed import StrPath, Unused + T = TypeVar("T") @@ -1666,7 +1678,7 @@ def test_path_subclassing(self, path: str, path_type: str): # Google cloud is not posix, for mocking purpose however we just # need a class that is a subclass of Path class MockGCSPath(PosixPath): - def __init__(self, *pathsegments: str): + def __init__(self, *pathsegments: StrPath, **kwargs: Unused): super().__init__(*pathsegments) def __str__(self): # __fspath__ calls __str__ by default diff --git a/typings/pyfakefs/fake_filesystem.pyi b/typings/pyfakefs/fake_filesystem.pyi index 037a020f..c822afbe 100644 --- a/typings/pyfakefs/fake_filesystem.pyi +++ b/typings/pyfakefs/fake_filesystem.pyi @@ -6,7 +6,7 @@ import sys from enum import Enum from typing import Any, AnyStr, Callable, NoReturn -from pyfakefs.fake_file import AnyFile, AnyFileWrapper, FakeFile +from pyfakefs.fake_file import AnyFile, AnyFileWrapper, FakeFile, FakeDirectory from pyfakefs.helpers import AnyPath, AnyString """A fake filesystem implementation for unit testing. @@ -91,7 +91,6 @@ class OSType(Enum): FakeNullFile = ... FakeFileFromRealFile = ... -FakeDirectory = ... FakeDirectoryFromRealDirectory = ... FakeFileWrapper = ... StandardStreamWrapper = ...